Category Archives: Expedition Reports & Updates

Photos, videos & reports from the field.

Field Report 2015-12-15: New DS18B20 1-Wire Sensor Chains Installed

A typical DS18b20 temperature string deployment

A typical deployment

The August deployment produced both success and failure from our 1st-generation temperature strings. We still managed to get both of those older units back on their feet with fresh batteries, and we add two beta units to the set.  I really had to scramble to get the new chains ready in time because we are spending more time on testing and calibration as I try to squeeze the best possible performance out of these humble DS18b20’s. It takes me about a day to solder and epoxy a  section with 8-12 sensors, so these instruments also represent a significant amount of build time. (note: the length of the wires in between nodes does not affect that time very much)

Although both of the alpha loggers passed the overnight tests following their first run, the shorter (25cm) chain developed a reading problem as soon as it was powered up. The fact that this error occurred before the unit went near the water tells me that it was either a sensor failure, or a problem with the connectors. I have been using Deans 1241 micro connectors between the segments because they seem really robust, but my gut tells me those break points could also add some signal reflection problems.

Here I am 'prospecting' for thermals by dangling a 24m chain from a life jacket and moving it around the cenote. I thik I will put a display screen on one of the next units to make this task easier.

We went hunting for potential deployment locations by dangling a 24m chain from a life jacket and moving it around the cenotes to generate profiles. I think I will put a display screen on one of the next units to make these ‘prospecting’ trips easier in the future.

The logger itself ran for the duration, but the log data was a string of the dreaded 85C (ie: 1360)  and ‘-1’ read errors.  Since these numbers are fairly distinctive, I will put an error check in code on startup to see if I can intercept this kind of problem in the future.  At least the pressure record from the MS5803 on the housing survived intact, and that sensor seems to be working again now that I have removed the Qsil silicone coating that I had over top of the sensor on the previous deployments.

I isolated the read fault to the first segment of the temperature sensor chain, and when that section was removed the rest of the sensors ran well enough. We decided to re-deploy the parts that were still running  (although the chain is now less than four meters long) and I brought the dodgy section home for some forensic testing. I am suspicious of the U-09LV urethane that I used on a few of the nodes, thinking that it’s higher moisture resistance might not compensate for the stiffness and overall durability of E-30CL.

Fortunately, the longer chain that we deployed in the deeper inland site performed well, giving us another record with sensors spanning the halocline:

raw data

Two months of raw DS18b20 output, Logger 46  (10m cable with 20 sensors). Note: the warmer temps shown at the top of this graph are from sensors deeper in the water column, while the cooler temperatures are from shallow sensors in fresh water

Even with relatively long 50 cm spacing, the large rain events of the season pushed the fresh/salt boundary around so much that several sensors (indicated here with 48pt moving averages) switched from the saline, to the fresh water, and then back again. It will be interesting to see if those bands tighten up, or spread out, after we apply our normalization factors.

New DS18b20 Temp strings ready to deploy.

This 6m x 24node chain has a 10m extension, allowing us to change sensor positions in the water column by simply tying off the excess.

After several meetings to obtain permission from the landowners, we managed to install our new set of DS18b20 temperature strings.  We decided to co-deploy a combination of high and low spatial resolution chains, so that we still have a good chance to get data, if one loggers dies.  Due to memory limitations, etc. I built them with twenty four sensor nodes per logger, and even with those spread out over 24m of cable, 3k3 pullup resistors are enough for the one wire communications. That’s aggressive enough to give me some concern about self-heating if I was doing multiple readings, but I figure that with the bus at 3.3v it probably just comes out in the wash.

This deployment site had significant amounts of hydrogen sulfide at depth which forms a visible layer that is shown well by these photos from Angelita.  It will be interesting to see how the chemistry affects our sensors. It certainly had an effect on me, as I was a little worse for wear after that dive.

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Field Report 2015-12-14: Re-install the Drip Monitoring Network

New tufa based installation.

These large soft formations often form around the tree roots that drill down into the caves from the surface.

I brought six new units to cover attrition of the older drip sensors, but with only one failure in the last round, the scheduled replacements left us with several ‘old but still working’ loggers in hand.  With so many good stalagmite-forming records in the bag, we decided to look at some of the amorphous flow-stone draperies on the periphery of the cave. It will be interesting to see if we can develop a sense of how much these sources contribute to the water draining into the cave.

Although I had not yet determined if the Masons RH experiment was working, we decided to re-installed those multi-probe logger since they capture both temperature and barometric data, which is still very useful information for the project.

A roof-top deployment is nearby, for comparison.

With a roof-top deployment nearby, we hope that comparisons with ground level units might provide some idea how much rain is evaporating before it even hits the ground…

With the success of the rain gauges, we decided to disperse those loggers to topside locations ranging as far as Tulum. I will build more for the next deployment, as we would eventually like to have surface rain gauges at all of our cave monitoring sites (precipitation is as relevant to the flow loggers as it is to the drip sensors!).  That’s a tall order, so I am happy that nearly all the units are delivering one-year or more operation on a set of batteries, so we no longer have to change them on every trip. As readers of this blog know, it’s been a long road bringing the project to the point where we can just leave the loggers in place if we run out of time, without loosing any data.




In all, there are now more than twenty five loggers in operation at Rio Secreto, which is the largest concentration of instruments we’ve ever had at one location. My hope is that the information we are gathering today helps to preserve their cave when the growing metropolis of Playa del Carmen reaches their doorstep.

The road out to Rio Secreto skirts the boarder of the largest limestone quarry in the area. A dramatic example of the different perspectives you encounter about how the natural resources of Mexico should be utilized. Of course, as a Canadian, I see exactly the same issues playing out back home...

The road out to Rio Secreto skirts the boarder of the largest limestone quarry in the area. A dramatic example of the different perspectives you encounter about how the natural resources of Mexico should be utilized. Of course, as a Canadian, I see exactly the same issues playing out back home…

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Field Report 2015-12-11: Flow sensors go Farther & Deeper

Baruch Figueroa-Zavala (from CEA) recently installed a new Cave Pearl flow sensor just down the coast from Akumal bay:

The latest reef deployment of the flow loggers

The latest reef deployment, 14m depth. (photo courtesy Baruch)

This marks our deepest ocean sensor deployment to date, and two backup bungees were added to ensure this unit does not get torn from it’s anchor like the last one we put outside the sheltered environment of the bay. The turbulence shadow from the reef will likely have some effect on the flow, and it will be interesting to see if this logger accumulates the same amount of bio-growth as the shallow water units…

Marco and I snorkeled out to retrieve both of the B-generation units in Akumal Bay, which were still running well. Both were heavily encrusted despite the thorough cleaning they had in August, and to my eye it looks like there might be even more gowning on them now than they had last time. I am wondering if the acid bath somehow roughens the surface, allowing more critters to get a foothold (?)  Of course it could just as easily be a result of some seasonal nutrient flux, so I leave it up to the biologists to comment. One thing that surprises me is that we are only now seeing the first evidence of a marine animal burrowing into the instruments, and they chose to attack the epoxy rather than the PVC. A subtle reminder that poly vinyl chloride is not the most benign substance in the world.

These units have been under water since the second flow meter deployment.  With twenty months of continuous operation under their belt, they are still producing solid results despite some fairly dodgy Dupont jumper cables that I would never use in my current builds. This makes me feel pretty good about all the laborious hand-sanding I did on those early housings:


Akumal Bay (North) Tilt angle (°) (from raw accelerometer readings)

It looks like a nice two-week tidal signal was coming through until the big rains took over the flow pattern. The temp sensor on-board shows how all that precipitation lowered the mid column water temperature in a pattern that is now beginning to look very familiar:


Unit B4: Akumal Bay (North) DS18b20 Temp (°C)

I really have to build myself a CTD to find out if the water temperature also tracks salinity, and if so, I wonder how that affects all the critters out there on the reef?

A few days later, after a good cleaning and a fresh set of batteries, we tried go back and  reinstall the flow sensors, only to find police waving everyone away from Akumal at the highway. For several days a group of protesters from the pueblo blocked roadway access in a vigorous dispute over access to the beach, so we had to leave the loggers with CEA staff for later deployment. Yet another reminder of  how the combined pressures of tourism and development completely dominate the regional dynamics, and I hope that the situation can be resolved in a way that preserves the bay for future generations.

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Field Report 2015-12-10: Sensor Precision vs Accuracy vs Drift

Testing multiple flow meter deployment configurations.

We compared different fin position configurations & three build generations on this deployment.

With drip sensor service under way, we started our usual round of dives to exchange the flow sensors. We often use our favorite coastal outflow as an equipment shakedown dive because it’s fairly shallow and we know the system so well at this point that it feels more like the project workshop than an actual cave. We monitor tide levels here with a pressure sensor, and we also had the 25cm DS18b20 temperature string in the system this time round (but I will report on those results later)

So close to the ocean, this system delivers tidal signals like ‘old faithful’, and we have another gorgeous data set (in triplicate!) to keep my favorite karst hydrologist happy:

Uncorrected Raw Tilt angle as a proxy for water flow velocity in one of our coastal outflow monitoring sites.

Raw Tilt angle in degrees (as a proxy for water flow velocity)

Those high flows line up nicely with the large rain events recorded at Rio Secreto, and with peak displacements above eighty degrees, I suspect that the drag fins are bumping the ceiling of the cave; clipping some of our high end. But that’s still a beautiful time series, and it reminds me that now I really have to get my hands on a logging ADCP so I can calibrate the 2″ housings to point velocity. Unfortunately past experience has already shown us that acoustics often don’t like being in caves with low ceilings, so I would also have to do that testing in some other system or get my hands on a concentrating beam ADV logger to avoid any reflection issues.

The other gorilla in the room is that age old question of accuracy vs precision. This shows up most clearly in the two temperature records from our pressure sensor, which sports a 12-bit Adafruit MCP9808, and a 24-bit MS5803-05BA (which also records temperature for it’s internal corrections) located right beside each other:

MCP9808 vs ms5803 temperature data...?

Temperature (°C): MCP9808 (Top)  vs MS5803 (Bottom)

That pesky pressure sensor....

That pesky pressure logger….

The bit depth limitation of the 9808 shows up pretty clearly against the 5803’s beefy ADC, but my dilemma is that that the factory calibration on the Adafruit sensor is ±0.25°C, while all the lovely data from the M.S. sensor comes with a quid pro quo of ±2.5°C.  I’d be happy to cherry pick diurnals out of the high rez record, but even without a trends over top it’s obvious that the two sensors have diverging behavior. (though both sensors claim great drift stability?). This is the kind of thing that drives a builder like me nuts because it hints that we might have another creeping problem like the TMP102 pressure sensitivity that nearly took out a whole generation of loggers. I think I will have to start recording the RTC temp register (which is protected inside the housing) so I have another data set to compare to these two surface mounted sensors.

What I would really like to know is if there was some way I could squeeze higher precision out of the 9808.  I keep finding off-hand references in the forums suggesting that if you average ~16 readings, you get another decimal place of resolution out of your sensor. But with temperature sensing IC’s doing massive amounts this when they convert 12-bit readings, they might already have reached the point of diminishing returns. This question is also relevant to the ubiquitous DS18b20’s we’re using, because they are so stable that 16 readings in a row usually just gives me the same number 16 times. Does this mean that averaging has already taken any bit-depth enhancing noise right out of the signal?

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Field Report 2015-12-08: The DIY Logging Rain Gauges Work!

Trish & Fernanda inspecting units before retrieval

Trish & Fernanda inspecting units before retrieval

We managed to squeeze in a short  fieldwork trip before the end of the year, and the growing number of loggers at Rio Secreto put that cave at the top of our list to give me enough time to service all the units.  It was also important that we get everything back into place before they were swamped by tourists wanting to spend their holidays in the sun, rather than shoveling snow.

I was very happy to see that only one single machine suffered a sensor failure, and this was one the surface drip units that we had cooked under the tropical sun during a previous deployment.  Some of our early monitoring stations are finally passing that critical one-year mark, so we can start to think about seasonal patterns in records that display this kind of short term variability:

Typical Drip Sensor record 2015, Rio Secreto cave

Drip count /15 min,  Station 10, Far Pool Cluster


I had no idea spiders were so fond of  living in climate stations…

We also had a several sensors on the surface, and I was really curious to see the the data from this first field deployment of the new rain gauges, given that so many of our cave records showed strong discontinuity events like the one above.  Not only did I want to see the quantitative data, I also wanted to know if the bottom shroud prevented the internal temperatures from going into to the 60°C range (which damaged several earlier loggers…)

And…. success! And both rain gauges were within 5% of each other, despite accumulations of bird poop & leaf litter, and one unit suffering from a slow tilt of nearly 10 degrees as the palapa roof shifted underneath it. With conversion ratios from my back-yard calibration, we were able to translate the drip counts directly into rain fall:

Rainfall (cm/day) data from one of our first rain gauge prototypes at rio Secreto

Rainfall (cm/day) from one of our first rain gauge prototypes at Rio Secreto

Trish had her doubts about this record initially, with so much rainfall occurring in what was supposed to be the local ‘dry’ season.  But after searching through data from nearby government weather stations, and comparing our surface record to the break-through events I was seeing in the drip data, we slowly became convinced that it had, in fact, been one of the rainiest dry seasons in quite a while.  We also had a beautiful temp record that showed the new cowlings pulled peak temperatures (inside the loggers) down by almost 20°C:

Rain gauge internal Temp from RTC registers.

Rain Gauge, Internal Temp (°C) from the DS3231 RTC register.

Hopefully this means that the SD cards are back in the safe operating zone, which I know from past failures is nowhere near the 85°C that Sandisk claims.

So the new rain gauges are working properly, adding another piece of hydrology instrumentation to the Cave Pearl lineup.  I would love to say that the Masons Hygrometers delivered another great success, but the analysis is turning out to be somewhat more complicated as the 96-98% RH variations pulled my wet bulb depressions right into the bit depth limit of the DS18b20’s , so I will have to keep you in suspense for a while as I chew on those numbers…

Addendum 2016-03-16

Well serves me right for counting my chickens: Turns out that the drip sensor based rain gauges suffer from spurious counts due to wind noise. But I’ve been running these guys at their highest sensitivity settings, so hopefully I can dial that back to reduce the problem. We also had the gauges on a soft palapa roof, which no doubt contributed to the problem.

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Cave Pearl Data Loggers at GSA 2015

We had two presentations at the Geological Society of America conference last weekend in Baltimore.  Trish spoke in the Karst Processes and Speleogenesis session about the challenges of new instrument development, and presented a snapshot of our growing long-term record which includes ocean sensors,  surface precipitation & cave drip monitors, with flow sensors inland and at coastal discharges:

Cave Pearl Logger deployment Record to Sept 2015

You can see attrition of the early prototypes pretty well in a graph like this.  We lost units from the 3rd generation of flow sensors due to epoxy failures, and much of the fourth failed due to pressure effects on our temperature sensors.  Despite having to wake for several hundred thousand processor interrupts,  the drip sensors are faring much better overall.  But I have been replacing them anyway, as the recent builds have much better power consumption. Even with improvements to each logger, you still reach a point where field logistics put a limit on how many units you can deploy with a small two person team.

While we aren’t at the whole catchment/watershed scale yet, we hope that our little DIY monitoring network will grow into the kind of coverage you see in Critical Zone Observatories.  Trish ended her talk by walking through some data from a very large storm event to show how it impacted the different monitoring stations. You could see the effect on people as they watched the individual sensor records building into a system wide picture of the hydrology.

Presenting the Cave Pearl loggers at the GSA conference 2015

There was a a lot of interest from younger academics, as they understand the potential for open source kit to help them compete with senior colleagues who can afford $5-10k for each piece of equipment.

That interest spilled over to the poster session the next day where I had a selection of different builds on display. I was a little embarrassed as many of these were rough early prototypes & bookshelf calibration units. (because all the really good loggers are currently out on deployment 🙂  There was a steady stream of people with questions that kept me at the poster all day and both of us were on deck for the huge crush of people at the end of the day. All that positive feedback was great for the ego, and it was especially nice to talk to people from other research groups working with the Arduinos. Each of us is tackling different questions, leading to a good diversity of hardware builds and approaches.

I think things are reaching critical mass because at this point many of the smaller independent projects people have been working on have seen enough field trials to cross the tipping point from rough prototypes to capable research equipment. DIY instrumentation will have a much larger presence at future conferences, and some of us have even started scheming about a whole session dedicated to it. If we can wedge it in between the teaching and the fieldwork schedule, perhaps next year we will bring the Pearls over to the AGU.


The conference generated enough interest to show up on the blog’s traffic: not so much as a change in the number of visitors, but as an increase in the number of pages being read:

I think pages per visitor is probably a better metric of interest, though I am sure humble stats like these don’t even count as a drop in internet bucket. But hey, you’ve got to start somewhere…

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Interview: Cave Pearl Project Team: 2015-09-20

Now that we have recovered from the last round of fieldwork, I finally managed to blow the dust off an old Macintosh in the basement and produce a little promo for the project:

Still needs some polish, but not bad for a few quick clips in the living room. My next task is to update my “How to build a data logger” posts to include all the new improvements.

Addendum 2015-08-24:

The new build series tutorials are now live to help folks get started.

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